Script to sum abundance of pathway across taxa

Microbial community profiling HUMAnN
1

Hello!
I’ve a question; is there a script for HUMAnN 2.0 that sums the abundance of all pathways per taxa?
For example:
L-arginine biosynthesis II (acetyl cycle)|g__Dorea.s__Dorea_longicatena: 30
L-arginine biosynthesis II (acetyl cycle)|g__Dorea.s__Dorea_sp_CAG_317: 22
L-arginine biosynthesis II (acetyl cycle)|g__Eggerthella.s__Eggerthella_lenta: 44

Can be summarised to:
L-arginine biosynthesis II (acetyl cycle): 96

Thank you for all replies!

2

The default HUMAnN output contains an unstratified community-total abundance for each pathway followed by the stratified versions. Unlike gene-level functions, the community-total pathway abundance is recomputed at the community level, and hence is not a true sum over the contributing taxa (for example, a pathway could be satisfied at the community level but never satisfied by any single species).